Mercurial > repos > iuc > mothur_parse_list

annotate parse.list.xml @ 1:033b821e30e1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:18:19 -0400
parents 0817dd05dbaf
children fe05fc98c62a
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0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_parse_list" name="Parse.list" version="@WRAPPER_VERSION@.0">
0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Generate a List file for each group</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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033b821e30e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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033b821e30e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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9 <command><![CDATA[
033b821e30e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
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13 ln -s "$otu" otu.dat &&
0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 ln -s "$group" group.dat &&
0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 ln -s "$count" count.dat &&
0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16
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17 echo 'parse.list(
0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 list=otu.dat,
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19 #if $label:
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20 label=${ str($label).replace(",","-") },
0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #end if
0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #if $count:
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23 count=count.dat,
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24 #end if
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25 group=group.dat
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26 )'
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27 | sed 's/ //g' ## mothur trips over whitespace
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28 | mothur
1
033b821e30e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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29 | tee mothur.out.log
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0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 ]]></command>
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31 <inputs>
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32 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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33 <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/>
0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include">
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35 <expand macro="labeloptions"/>
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36 </param>
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37 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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38 </inputs>
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39 <outputs>
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40 <expand macro="logfile-output"/>
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41 <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: listfiles per group and label">
0817dd05dbaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.list" format="mothur.list"/>
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43 </collection>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="otu" value="amazon.an.list"/>
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48 <param name="group" value="amazon.groups"/>
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49 <output_collection name="listfiles" count="72">
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50 <element name="pasture.0.21" md5="5c803fd0f0e1de69c51048e02bc02e65" ftype="mothur.list"/>
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51 </output_collection>
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52 <expand macro="logfile-test"/>
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53 </test>
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54 <test>
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55 <param name="otu" value="amazon.an.list"/>
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56 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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57 <param name="label" value="0.03,0.05"/>
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58 <output_collection name="listfiles" count="4"/>
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59 <expand macro="logfile-test"/>
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60 </test>
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61 </tests>
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62 <help>
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63 <![CDATA[
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64
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65 @MOTHUR_OVERVIEW@
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66
1
033b821e30e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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67 **Command Documentation**
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68
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69 The parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile.
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70
1
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71 .. _list: https://www.mothur.org/wiki/List_file
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72 .. _group: https://www.mothur.org/wiki/Group_file
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73 .. _parse.list: https://www.mothur.org/wiki/Parse.list
0
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74
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75 v.1.19.0: Updated to mothur 1.33, added count parameter
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76 ]]>
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77 </help>
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78 <expand macro="citations"/>
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79 </tool>